Our expert says:
This is tricky, because by now, your legs should have adapted enough to be able to handle the training. The muscle stiffness and pain is pretty common when first starts running, but it usually goes away. Does your worst muscle soreness come after that long run? Or do the short runs also affect you? It might be that you're simply not recovering because your training intensity is too high - persistent muscle soreness is a symptom of too much or too hard training. And remember that training by itself is not the only "stress" you are dealing with - it could be other things in your life too.
I'd also look at diet - enough carbohydrates and proteins, because there is some research that shows that insufficient energy intake compromises recovery.
But I think the main thing is training. And while it may be frustrating, the fact that this is a new programme is an important clue, since it might show that this new plan is a problem for you. Either shorter runs or slower run might be the order of the day.
So I'd back off, just for a week or two, see what happens and then build up again. Maybe instead of a usual 45 minute run, you need to jog 3 minutes, walk 2 minutes, and repeat 9 times. See what it does. You just need to adapt to the training, and at the moment, that's what doesn't seem to be happening.
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